OMPdb is a dedicated database that contains

beta barrel In protein structures, a beta barrel is a beta sheet composed of tandem repeats that twists and coils to form a closed toroidal structure in which the first strand is bonded to the last strand (hydrogen bond). Beta-strands in many beta-barrels are ...

(β-barrel) outer membrane proteins from

Gram-negative bacteria Gram-negative bacteria are bacteria that do not retain the crystal violet stain used in the Gram staining method of bacterial differentiation. They are characterized by their cell envelopes, which are composed of a thin peptidoglycan cell wall ...

. Such proteins are responsible for a broad range of important functions, like

passive Passive may refer to: * Passive voice, a grammatical voice common in many languages, see also Pseudopassive * Passive language, a language from which an interpreter works * Passivity (behavior), the condition of submitting to the influence of o ...

nutrient uptake,

active transport In cellular biology, ''active transport'' is the movement of molecules or ions across a cell membrane from a region of lower concentration to a region of higher concentration—against the concentration gradient. Active transport requires cellul ...

of large molecules, protein secretion, as well as

adhesion Adhesion is the tendency of dissimilar particles or surfaces to cling to one another ( cohesion refers to the tendency of similar or identical particles/surfaces to cling to one another). The forces that cause adhesion and cohesion can b ...

host cells In biology and medicine, a host is a larger organism that harbours a smaller organism; whether a parasitic, a mutualistic, or a commensalist ''guest'' (symbiont). The guest is typically provided with nourishment and shelter. Examples include a ...

, through which bacteria expose their

virulence Virulence is a pathogen's or microorganism's ability to cause damage to a host. In most, especially in animal systems, virulence refers to the degree of damage caused by a microbe to its host. The pathogenicity of an organism—its ability to ...

activity. Their biological importance together with the inadequate annotation and classification found in public databases, urges the need for intensive studies and accurate data collection regarding β-barrel proteins. Information included in OMPdb consists of

sequence In mathematics, a sequence is an enumerated collection of objects in which repetitions are allowed and order matters. Like a set, it contains members (also called ''elements'', or ''terms''). The number of elements (possibly infinite) is calle ...

data, as well as annotation for structural characteristics (such as the transmembrane segments), literature references and links to other public databases, features that are unique worldwide. We also offer information regarding the existence of a 3D-structure of a given protein, if it is deposited in the PDB database. A list of protein entries with solved 3D-structure can be also found in each family entry page, when applicable. Along with the database, a collection of profile

Hidden Markov Models A hidden Markov model (HMM) is a statistical Markov model in which the system being modeled is assumed to be a Markov process — call it X — with unobservable ("''hidden''") states. As part of the definition, HMM requires that there be an ob ...

, originating mainly from the PFAM database, that were shown to be characteristic for β-barrel outer membrane proteins was also compiled. This set, when used in combination with the recently presente
PRED-TMBB2
algorithm, will serve as a powerful tool in terms of discrimination and classification of novel β-barrel proteins and whole-proteome analyses. The web interface of OMPdb offers the user the ability not only to view the available data, but also to submit advanced queries for

text search In computer science, string-searching algorithms, sometimes called string-matching algorithms, are an important class of string algorithms that try to find a place where one or several strings (also called patterns) are found within a larger stri ...

within the database's protein entries or perform protein and domain searches. The most up-to-date version of the database can be downloaded in various formats (flat text,

XML Extensible Markup Language (XML) is a markup language and file format for storing, transmitting, and reconstructing arbitrary data. It defines a set of rules for encoding documents in a format that is both human-readable and machine-readable ...

format or raw

FASTA FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program ...

sequences). In the download page, the user may download the complete dataset of β-barrel proteins, which is compiled following the regular updates of th
PDBTM
database, th
OPM
database and th
list
of membrane proteins of known 3D-structure fro
Stephen White
s laboratory at

UC Irvine UC may refer to: Arts and entertainment * '' University Challenge'', a popular British quiz programme airing on BBC Two ** ''University Challenge (New Zealand)'', the New Zealand version of the British programme * Universal Century, one of the t ...

. During 11–12 August 2014, OMPdb participated at the Protein Bioinformatics and Community Resources retreat in the Wellcome Trust Conference Centre, brought together the principal investigators of several specialized protein resources as well as those from protein databases from the large Bioinformatics centres. During this meeting some common key challenges involved in creating and maintaining such resources were discussed, along with various approaches to address them. An important outcome was the creation of a Specialist Protein Resource Network that aims to improve coordination of the activities of its member resources.

References

External links

* http://www.ompdb.org/ Biological databases Protein structure Protein folds Gram-negative bacteria {{Biodatabase-stub